Initially conceived by the President of the United Federation as a means of developing an "immortality formula", Project Shadow was apparently named so as to remind the researchers of the need for absolute secrecy in their work. Professor Gerald Robotnik, considered one of the most brilliant minds of the time, was personally requested to assist in making it a reality. Prof. Gerald realized he might be able to co-opt the program in order to find a cure for Neuro-Immune Deficiency Syndrome, an incurable disease afflicting his granddaughter, Maria. With this motivation, he agreed and led the project on the Space Colony ARK, an orbiting facility isolated from earth.
As the project progressed, Gerald made contact with an alien life form known as Black Doom, the leader of the Black Arms race. Doom assisted Gerald with his research, going so far as to provide genetic material for the project in the form of his blood. Gerald also studied the Chaos Emeralds, producing Chaos Drives to test infinite energy of the Emeralds on living tissue. The project produced Biolizard, a creature containing many of the desired traits: regeneration, restoration, self-reproduction. However, it required a life-support machine to remain viable. In addition, the Biolizard also grew at a rate that even he did not expect—gaining a size of 2.7 meters and 350kg in just a couple of days. Likewise, the Biolizard possessed a low learning rate at that time, making it more comparable to a primitive animal. It was also sensitive to temperature changes and (at the time of its analysis) was not strong enough to walk, although its tail and neck were strong. It also contained an organ that was installed into it to start the Chaos Control. As the prototype proved unruly, development shifted to a more intelligent subject - Shadow the Hedgehog - who formed a friendship with Maria.
Over time, the nature of the project made the government uneasy, and they considered cutting funding. During this time, the professor also discovered an ancient robot called a Gizoid, which could mimic combat abilities. Gerald offered the Gizoid to the government as a bribe so he could keep Project Shadow going. Unfortunately, the bribe did not work. Although Project Shadow was virtually complete, Gerald realized that his successful contact with the Black Comet prompted too much fear. The military forcibly shut down the space colony, attacking any remaining resistance. During the invasion, Maria helped Shadow the Hedgehog to escape, which resulted in her getting shot by a soldier. With her final words, she safely ejected him to the planet by Maria. With Maria and Shadow both announced dead, Prof. Gerald went mad - he eventually recovered Shadow and brainwashed him to carry out his revenge, but they were captured by the military. Shadow was placed in stasis, while Gerald was to be executed.
In Shadow the Hedgehog, it is revealed that Black Doom had his own, non-humanitarian agenda in contributing to Project Shadow. While the President wanted an immortality formula and Gerald wanted a cure for Neuro-Immune Deficiency Syndrome, Black Doom intended the program to produce an agent who would gather the Chaos Emeralds for him on the inner solar system, fifty years later. In this, Doom is actually the only one to get what he wanted from Project Shadow–although it backfires spectacularly on him, in that Shadow, despite delivering the Emeralds, fulfills his promise to the girl he was created for, putting his past behind him to become Super Shadow and defeat Devil Doom. Subsequently, the ARK's Eclipse Cannon obliterated the Black Comet.
↑The report on the Biolizard, shown during a cutscene to Shadow by Rouge the Bat, mentioned these.